| 1. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
|
|
| 2. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
|
|
| 3. |
- Abolfathi, Bela, et al.
(författare)
-
The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
-
Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
-
Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
|
|
| 4. |
- Chu, Ming, et al.
(författare)
-
Accurate capacitance-voltage characterization of organic thin films with current injection*
- 2021
-
Ingår i: Chinese Physics B. - : IOP PUBLISHING LTD. - 1674-1056. ; 30:8
-
Tidskriftsartikel (refereegranskat)abstract
- To deal with the invalidation of commonly employed series model and parallel model in capacitance-voltage (C-V) characterization of organic thin films when current injection is significant, a three-element equivalent circuit model is proposed. On this basis, the expression of real capacitance in consideration of current injection is theoretically derived by small-signal analysis method. The validity of the proposed equivalent circuit and theoretical expression are verified by a simulating circuit consisting of a capacitor, a diode, and a resistor. Moreover, the accurate C-V characteristic of an organic thin film device is obtained via theoretical correction of the experimental measuring result, and the real capacitance is 35.7% higher than the directly measured capacitance at 5-V bias in the parallel mode. This work strongly demonstrates the necessity to consider current injection in C-V measurement and provides a strategy for accurate C-V characterization experimentally.
|
|
| 5. |
- Fan, Zhaozhong, et al.
(författare)
-
Oxygen-Bridged Indium-Nickel Atomic Pair as Dual-Metal Active Sites Enabling Synergistic Electrocatalytic CO2 Reduction
- 2023
-
Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 62:7
-
Tidskriftsartikel (refereegranskat)abstract
- Single-atom catalysts offer a promising pathway for electrochemical CO2 conversion. However, it is still a challenge to optimize the electrochemical performance of dual-atom catalysts. Here, an atomic indium-nickel dual-sites catalyst bridged by an axial oxygen atom (O-In-N6-Ni moiety) was anchored on nitrogenated carbon (InNi DS/NC). InNi DS/NC exhibits superior CO selectivity with Faradaic efficiency higher than 90 % over a wide potential range from −0.5 to −0.8 V versus reversible hydrogen electrode (vs. RHE). Moreover, an industrial CO partial current density up to 317.2 mA cm−2 is achieved at −1.0 V vs. RHE in a flow cell. In situ ATR-SEIRAS combined with theory calculations reveal that the synergistic effect of In-Ni dual-sites and O atom bridge not only reduces the reaction barrier for the formation of *COOH, but also retards the undesired hydrogen evolution reaction. This work provides a feasible strategy to construct dual-site catalysts towards energy conversion.
|
|
| 6. |
|
|
| 7. |
- Guo, Xiao-Hua, et al.
(författare)
-
Advanced glycation end products induce actin rearrangement and subsequent hyperpermeability of endothelial cells
- 2006
-
Ingår i: APMIS : acta pathologica, microbiologica, et immunologica Scandinavica. - : Wiley. - 1600-0463 .- 0903-4641. ; 114:12, s. 874-883
-
Tidskriftsartikel (refereegranskat)abstract
- This study aimed to determine the effects of advanced glycation end products (AGEs) on endothelial cytoskeleton morphology and permeability, and to detect the underlying signaling mechanisms involved in these responses. Cultured endothelial cells (ECs) were exposed to AGE-modified human serum albumin (AGE-HSA), and EC cytoskeletal changes were evaluated by observing fluorescence of F-actin following ligation with labeled antibodies. Endothelial permeability was detected by measuring the flux of TRITC-albumin across the EC monolayers. To explore the signaling pathways behind AGE-induced EC alteration, ECs were treated with either soluble anti-AGE receptor (RAGE) IgG, or the MAPK inhibitors PD98059 and SB203580 before AGE-HSA administration. To further elucidate possible involvement of the ERK and p38 pathways in AGE-induced EC changes, adenovirus-carried recombinant constitutive dominant-negative forms of upstream ERK and p38 kinases, namely MEK1(A) and MKK6b(A), were pre-infected into ECs 24 h prior to AGE-HSA exposure. AGE-HSA induced actin cytoskeleton rearrangement, as well as EC hyperpermeability, in a dose and time-dependent manner. The effects were attenuated in cells pretreated with anti-RAGE IgG, PD98059 or SB203580, respectively. EC pre-infection with MEK1(A) and MKK6b(A) also alleviated the effect of AGEs. Furthermore, adenovirus-mediated administration of activated forms of either MEK1 or MKK6b alone induced rearrangement of F-actin and hyperpermeability. The results indicate that ERK and p38 MAPK play important roles in the mediation of AGE-induced EC barrier dysfunction associated with morphological changes of the F-actin.
|
|
| 8. |
- Hou, Jungang, et al.
(författare)
-
Electrical Behavior and Electron Transfer Modulation of Nickel-Copper Nanoalloys Confined in Nickel-Copper Nitrides Nanowires Array Encapsulated in Nitrogen-Doped Carbon Framework as Robust Bifunctional Electrocatalyst for Overall Water Splitting
- 2018
-
Ingår i: Advanced Functional Materials. - : Wiley-VCH Verlagsgesellschaft. - 1616-301X .- 1616-3028. ; 28:37
-
Tidskriftsartikel (refereegranskat)abstract
- Probing robust electrocatalysts for overall water splitting is vital in energy conversion. However, the catalytic efficiency of reported catalysts is still limited by few active sites, low conductivity, and/or discrete electron transport. Herein, bimetallic nickel-copper (NiCu) nanoalloys confined in mesoporous nickel-copper nitride (NiCuN) nanowires array encapsulated in nitrogen-doped carbon (NC) framework (NC-NiCu-NiCuN) is constructed by carbonization-/nitridation-induced in situ growth strategies. The in situ coupling of NiCu nanoalloys, NiCuN, and carbon layers through dual modulation of electrical behavior and electron transfer is not only beneficial to continuous electron transfer throughout the whole system, but also promotes the enhancement of electrical conductivity and the accessibility of active sites. Owing to strong synergetic coupling effect, such NC-NiCu-NiCuN electrocatalyst exhibits the best hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) performance with a current density of 10 mA cm(-2) at low overpotentials of 93 mV for HER and 232 mV for OER, respectively. As expected, a two-electrode cell using NC-NiCu-NiCuN is constructed to deliver 10 mA cm(-2) water-splitting current at low cell voltage of 1.56 V with remarkable durability over 50 h. This work serves as a promising platform to explore the design and synthesis of robust bifunctional electrocatalyst for overall water splitting.
|
|
| 9. |
- Hou, Jungang, et al.
(författare)
-
Rational Design of Nanoarray Architectures for Electrocatalytic Water Splitting
- 2019
-
Ingår i: Advanced Functional Materials. - : Wiley-VCH Verlagsgesellschaft. - 1616-301X .- 1616-3028. ; 29:20
-
Forskningsöversikt (refereegranskat)abstract
- Electrochemical water splitting is recognized as a practical strategy for impelling the transformation of sustainable energy sources such as solar energy from electricity to clean hydrogen fuel. To actualize the large-scale hydrogen production, it is paramount to develop low-cost, earth-abundant, efficient, and stable electrocatalysts. Among those electrocatalysts, alternative architectural arrays grown on conductive substrates have been proven to be highly efficient toward water splitting due to large surface area, abundant active sites, and synergistic effects between the electrocatalysts and the substrates. Herein, the advancement of nanoarray architectures in electrocatalytic applications is reviewed. The categories of different nanoarrays and the reliable and versatile synthetic approaches of electrocatalysts are summarized. A unique emphasis is highlighted on the promising strategies to enhance the electrocatalytic activities and stability of architectural arrays by component manipulation, heterostructure regulation, and vacancy engineering. The intrinsic mechanism analysis of electronic structure optimization, intermediates' adsorption facilitation, and coordination environments' amelioration is also discussed with regard to theoretical simulation and in situ identification. Finally, the challenges and opportunities on the valuable directions and promising pathways of architectural arrays toward outstanding electrocatalytic performance are provided in the energy conversion field, facilitating the development of promising water splitting systems.
|
|
| 10. |
- Hou, Jie, et al.
(författare)
-
Subspace Hammerstein Model Identification under Periodic Disturbance
- 2018
-
Ingår i: IFAC-PapersOnLine. - : Elsevier B.V.. - 2405-8963.
-
Konferensbidrag (refereegranskat)abstract
- In this paper, a subspace identification method is proposed for Hammerstein systems under periodic disturbance. By using the linear superposition principle to decompose the periodic disturbance response from the deterministic system response, an orthogonal projection is established to eliminate the disturbance effect. The unknown disturbance period can be estimated by defining an objective function of output prediction error for minimization. Correspondingly, a singular value decomposition (SVD) based algorithm is given to estimate the observability matrix and the lower triangular block-Toeplitz matrix. The state matrices A and C are subsequently retrieved from the estimated observability matrix via a shift-invariant algorithm, while the input matrix B and the nonlinear input function parameters are retrieved from the estimated lower triangular block-Toeplitz matrix by an SVD approach. Consistent estimation of the observability matrix and the lower triangular block-Toeplitz matrix is analyzed. An illustrative example is shown to demonstrate the effectiveness of the proposed identification method.
|
|
